Back in January, at the end of my post on Illumina's new machine lineup I speculated whether Illumina might see a niche for a lower cost, lower throughput sequencing system that would slot below the MiSeq in their lineup. Such an instrument, I posited, might go after applications in biosurveilance and diagnostics where relatively small amounts of data are needed quickly. I speculated that perhaps a smaller instrument with less expensive optics could compete in this arena, which is heating up due to Oxford Nanopore and the growing acceptance of DNA-based diagnostics. As luck would have it, a few days later Molly He, Mostafa Ronaghi and colleagues at Illumina actually published a proof-of-concept paper for just such an instrument. Unlike many sequencing technology PoC papers, this one demonstrates feasibility of reading actual templates (phiX rides again!).
A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery
Tuesday, May 26, 2015
Wednesday, May 20, 2015
London Calling Wrap-Up
The second, and final, day of Oxford Nanopore's London Calling conference concluded last Friday -- and I'm behind on writing it up. Some of that was due to travel (and the wrong power supply going on the trip) and post-trip exhaustion, but failing to finish this last night was pure slacking. That route was shut down when one reader asked when I'd get things done. Anyway, I again organized the activity into a storify story as I did for the first day of the conference. I'm going to go into less detail on individual presentations below and instead engage in the vice of far-ranging speculation.
Friday, May 15, 2015
London Calling Day 1: Highlights
Oxford Nanopore's London Calling conference kicked off today; I've Storified a large collection of Tweets from it, covering today up through about dinner. I'll summarize some highlights below
Wednesday, May 13, 2015
Oxford Nanopore's London Calling: Pre-meeting speculation
Oxford Nanopore's London Calling confab starts up in a matter of hours. Alas, several issues scotched my plans to attend (not only does it promise to be an exciting conference, but I simply love exploring London on foot). It is worth emphasizing that the MinION devices and consumbables have been out in the wild for not quite 11 months at this time. In that time, Oxford has dealt with a wide variety of technical and logistical headaches. While performance is still variable, many MAP participants are forging forward and the available tools for nanopore data continue to grow. London Calling will likely bring a burst of new announcements; Oxford's Clive Brown has been giving talks recently but has promised that exciting stuff has been reserved for the confab. Below is a set of semi-informed speculations calling out likely happenings, mostly based on Clive's recent presentations and tweets.
PacBio's New Sample Prep Plan: Too Late to the Dance?
Pacific Biosciences had a string of announcements around its earnings release last week. Of particular interest is a collaboration with RainDance to develop a new sample preparation system for generating long synthetic reads from minuscule inputs. If some of that sounds familiar, the loose outline in the press release suggests an approach similar to that of 10X. But is this proposed system arriving too late to the party?
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